RNA-Seq Transcript Assembly using the ABySS Algorithm


Trans-ABySS is an extension of the ABySS program which is designed to do sequence assembly for RNA-seq transcript sequences. For more information, refer to the main website.

Using Trans-ABySS on RCC Systems

This program does not require a separate module to be loaded. However, the entire file path to the executable must be typed out in order to get the program to run. This can be done as follows:

/opt/hpc/gnu/libexec/trans-ABySS/transabyss OPTIONS FILES

Running Trans-ABySS in Parallel

Trans-ABySS has two different parallel modes, the OpenMP mode and the MPI mode. Further information can be found on their tutorial website here. Using this on HPC can be done using the following commands:

module load gnu-openmpi

# For the OpenMP version
/opt/hpc/gnu/libexec/trans-ABySS/transabyss --threads N_THREADS OPTIONS FILES

# For the MPI version
mpirun -np N_PROCESSES /opt/hpc/gnu/libexec/trans-ABySS/transabyss --mpi N_PROCESSES OPTIONS FILES

The MPI version can also be run using the SLURM job submission system. This can be done using a script like the following:


#SBATCH --job-name="TransABySS_MPI"
#SBATCH --mail-type=ALL
#SBATCH -n 4
#SBATCH -p genacc_q
#SBATCH -t 14-00:00:00
#SBATCH --mem-per-cpu=3900M

module load gnu-openmpi

mpirun -np 4 /opt/hpc/gnu/libexec/trans-ABySS/transabyss --mpi 4 OPTIONS FILES